Bright ligand-activatable fluorescent protein for high-quality multicolor live-cell super-resolution microscopy

We introduce UnaG as a green-to-dark photoswitching fluorescent protein capable of high-quality super-resolution imaging with photon numbers equivalent to the brightest photoswitchable red protein. UnaG only fluoresces upon binding of a fluorogenic metabolite, bilirubin, enabling UV-free reversible photoswitching with easily controllable kinetics and low background under Epi illumination. The on- and off-switching rates are controlled by the concentration of the ligand and the excitation light intensity, respectively, where the dissolved oxygen also promotes the off-switching. The photo-oxidation reaction mechanism of bilirubin in UnaG suggests that the lack of ligand-protein covalent bond allows the oxidized ligand to detach from the protein, emptying the binding cavity for rebinding to a fresh ligand molecule. We demonstrate super-resolution single-molecule localization imaging of various subcellular structures genetically encoded with UnaG, which enables facile labeling and simultaneous multicolor imaging of live cells. UnaG has the promise of becoming a default protein for high-performance super-resolution imaging. Photoconvertible proteins occupy two color channels thereby limiting multicolour localisation microscopy applications. Here the authors present UnaG, a new green-to-dark photoswitching fluorescent protein for super-resolution imaging, whose activation is based on a noncovalent binding with bilirubin

Multiplexed and scalable super-resolution imaging of three-dimensional protein localization in size-adjustable tissues

The biology of multicellular organisms is coordinated across multiple size scales, from the subnanoscale of molecules to the macroscale, tissue-wide interconnectivity of cell populations. Here we introduce a method for super-resolution imaging of the multiscale organization of intact tissues. The method, called magnified analysis of the proteome (MAP), linearly expands entire organs fourfold while preserving their overall architecture and three-dimensional proteome organization. MAP is based on the observation that preventing crosslinking within and between endogenous proteins during hydrogel-tissue hybridization allows for natural expansion upon protein denaturation and dissociation. The expanded tissue preserves its protein content, its fine subcellular details, and its organ-scale intercellular connectivity. We use off-the-shelf antibodies for multiple rounds of immunolabeling and imaging of a tissue's magnified proteome, and our experiments demonstrate a success rate of 82% (100/122 antibodies tested). We show that specimen size can be reversibly modulated to image both inter-regional connections and fine synaptic architectures in the mouse brain.United States. National Institutes of Health (1-U01-NS090473-01

A Measurement of Rb using a Double Tagging Method

The fraction of Z to bbbar events in hadronic Z decays has been measured by the OPAL experiment using the data collected at LEP between 1992 and 1995. The Z to bbbar decays were tagged using displaced secondary vertices, and high momentum electrons and muons. Systematic uncertainties were reduced by measuring the b-tagging efficiency using a double tagging technique. Efficiency correlations between opposite hemispheres of an event are small, and are well understood through comparisons between real and simulated data samples. A value of Rb = 0.2178 +- 0.0011 +- 0.0013 was obtained, where the first error is statistical and the second systematic. The uncertainty on Rc, the fraction of Z to ccbar events in hadronic Z decays, is not included in the errors. The dependence on Rc is Delta(Rb)/Rb = -0.056*Delta(Rc)/Rc where Delta(Rc) is the deviation of Rc from the value 0.172 predicted by the Standard Model. The result for Rb agrees with the value of 0.2155 +- 0.0003 predicted by the Standard Model.Comment: 42 pages, LaTeX, 14 eps figures included, submitted to European Physical Journal

Measurement of the B+ and B-0 lifetimes and search for CP(T) violation using reconstructed secondary vertices

The lifetimes of the B+ and B-0 mesons, and their ratio, have been measured in the OPAL experiment using 2.4 million hadronic Z(0) decays recorded at LEP. Z(0) --> b (b) over bar decays were tagged using displaced secondary vertices and high momentum electrons and muons. The lifetimes were then measured using well-reconstructed charged and neutral secondary vertices selected in this tagged data sample. The results aretau(B+) = 1.643 +/- 0.037 +/- 0.025 pstau(Bo) = 1.523 +/- 0.057 +/- 0.053 pstau(B+)/tau(Bo) = 1.079 +/- 0.064 +/- 0.041,where in each case the first error is statistical and the second systematic.A larger data sample of 3.1 million hadronic Z(o) decays has been used to search for CP and CPT violating effects by comparison of inclusive b and (b) over bar hadron decays, No evidence fur such effects is seen. The CP violation parameter Re(epsilon(B)) is measured to be Re(epsilon(B)) = 0.001 +/- 0.014 +/- 0.003and the fractional difference between b and (b) over bar hadron lifetimes is measured to(Delta tau/tau)(b) = tau(b hadron) - tau((b) over bar hadron)/tau(average) = -0.001 +/- 0.012 +/- 0.008

Colouration and Colour Changes of the Fiddler Crab, Uca capricornis: A Descriptive Study

Colour changes in animals may be triggered by a variety of social and environmental factors and may occur over a matter of seconds or months. Crustaceans, like fiddler crabs (genus Uca), are particularly adept at changing their colour and have been the focus of numerous studies. However, few of these studies have attempted to quantitatively describe the individual variation in colour and pattern or their adaptive significance. This paper quantitatively describes the colour patterns of the fiddler crab Uca capricornis and their ability to change on a socially significant timescale. The most dramatic changes in colour pattern are associated with moulting. These ontogenetic changes result in a general reduction of the colour pattern with increasing size, although females are more colourful and variable than similarly-sized males. Uca capricornis are also capable of rapid colour changes in response to stress, but show no endogenous rhythms associated with the semilunar and tidal cycles commonly reported in other fiddler crabs. The extreme colour polymorphism and the relative stability of the colour patterns in Uca capricornis are consistent with their use in visually mediated mate recognition

Efficacy of insect larval meal to replace fish meal in juvenile barramundi, Lates calcarifer reared in freshwater

The present experiment was conducted to evaluate the efficacy of dietary protein from black soldier fly, Hermetia illucens, larval meal (BSFL) to replace fish meal (FM) protein in juvenile barramundi, Lates calcarifer. Larvae of black soldier fly were fed with the underutilised crop, sesbania, Sesbania grandiflora. Five isonitrogenous (44% crude protein) and isocaloric (16.0 kJ available energy/g) experimental diets were formulated to replace FM using processed BSFL meal at 0 (control), 25% (BSFL25), 50% (BSFL50), 75% (BSFL75) and 100% (BSFL100). Data for proximate and amino acid analysis suggested BSFL meal as an inferior protein ingredient than FM, but parallel to soybean meal. At the end of 8 weeks of fish feeding trial, there were no significant differences in the average weight gain (WG) and specific growth rate among the group of fish-fed control, BSFL25 and BSFL50 diets (P < 0.05). Although numerical differences were recorded in the fish whole-body proximate composition, crude protein and moisture content were not much affected by the different dietary treatments. Essential amino acids including arginine, histidine, lysine and methionine were found to be higher in the whole body of fish-fed BSFL100 diet. Broken line regression analysis of average WG showed an optimum FM replacement level of 28.4% with BSFL meal. Therefore, the present experiment clearly demonstrates that the maximal dietary inclusion level of BSFL meal as FM protein replacer for the optimum growth of juvenile barramundi reared in freshwater could be greater than 28.4% but less than 50%, without any adverse effects on the fish whole-body proximate and amino acid composition

Expected Performance of the ATLAS Experiment - Detector, Trigger and Physics

A detailed study is presented of the expected performance of the ATLAS detector. The reconstruction of tracks, leptons, photons, missing energy and jets is investigated, together with the performance of b-tagging and the trigger. The physics potential for a variety of interesting physics processes, within the Standard Model and beyond, is examined. The study comprises a series of notes based on simulations of the detector and physics processes, with particular emphasis given to the data expected from the first years of operation of the LHC at CERN

Moving out of the shadows: accomplishing bisexual motherhood

Our qualitative study explored the ways in which bisexual mothers came to identify as such and how they structured their relationships and parenting within hetero-patriarchal society. The experiences of seven self-identified White bisexual women (aged from 28 to 56-years-old) from across England and the Republic of Ireland were investigated through semi-structured interviews. Participants’ children were aged 8 months to 28 years old at the time of their interviews. A thematic narrative analysis highlighted the following issues that participants had encountered in constructing their self-identity: prioritizing children; connecting and disconnecting with others and finessing self-definition; questioning societal relationship expectations. Nevertheless, participants varied considerably in how each of the themes identified were reflected in their lives, in particular depending upon each participant’s interpretation of her local social context. Both motherhood and self-identifying as bisexual gave a sense of meaning and purpose to participants’ life stories, although participants sometimes foregrounded their commitment to their children even at a personal cost to their bisexual identity. Using three different theoretical perspectives from feminist theory, queer theory and life course theory, the narratives analysed revealed ways in which bisexual motherhood not only had been influenced both intentionally and unintentionally by heteronormative expectations but also had directly and indirectly challenged these expectations

Feedforward Inhibition and Synaptic Scaling – Two Sides of the Same Coin?

Feedforward inhibition and synaptic scaling are important adaptive processes that control the total input a neuron can receive from its afferents. While often studied in isolation, the two have been reported to co-occur in various brain regions. The functional implications of their interactions remain unclear, however. Based on a probabilistic modeling approach, we show here that fast feedforward inhibition and synaptic scaling interact synergistically during unsupervised learning. In technical terms, we model the input to a neural circuit using a normalized mixture model with Poisson noise. We demonstrate analytically and numerically that, in the presence of lateral inhibition introducing competition between different neurons, Hebbian plasticity and synaptic scaling approximate the optimal maximum likelihood solutions for this model. Our results suggest that, beyond its conventional use as a mechanism to remove undesired pattern variations, input normalization can make typical neural interaction and learning rules optimal on the stimulus subspace defined through feedforward inhibition. Furthermore, learning within this subspace is more efficient in practice, as it helps avoid locally optimal solutions. Our results suggest a close connection between feedforward inhibition and synaptic scaling which may have important functional implications for general cortical processing

The Chemical Information Ontology: Provenance and Disambiguation for Chemical Data on the Biological Semantic Web

Cheminformatics is the application of informatics techniques to solve chemical problems in silico. There are many areas in biology where cheminformatics plays an important role in computational research, including metabolism, proteomics, and systems biology. One critical aspect in the application of cheminformatics in these fields is the accurate exchange of data, which is increasingly accomplished through the use of ontologies. Ontologies are formal representations of objects and their properties using a logic-based ontology language. Many such ontologies are currently being developed to represent objects across all the domains of science. Ontologies enable the definition, classification, and support for querying objects in a particular domain, enabling intelligent computer applications to be built which support the work of scientists both within the domain of interest and across interrelated neighbouring domains. Modern chemical research relies on computational techniques to filter and organise data to maximise research productivity. The objects which are manipulated in these algorithms and procedures, as well as the algorithms and procedures themselves, enjoy a kind of virtual life within computers. We will call these information entities. Here, we describe our work in developing an ontology of chemical information entities, with a primary focus on data-driven research and the integration of calculated properties (descriptors) of chemical entities within a semantic web context. Our ontology distinguishes algorithmic, or procedural information from declarative, or factual information, and renders of particular importance the annotation of provenance to calculated data. The Chemical Information Ontology is being developed as an open collaborative project. More details, together with a downloadable OWL file, are available at http://code.google.com/p/semanticchemistry/ (license: CC-BY-SA)